Based on the footage I've seen from Comic-con, it definitely looks like they're going that route.
I once saw a t-shirt that read "Jesus will return, and we'll kill him again."
The sad fact is that with our society the way it is, if Christ did return, most of his Christians would think he was a nutcase and have him locked up. Once he started performing miracles, our government would probably send the military to take him out....
...similar to what I'm seeing in the Comic-con footage of Superman. If any messiah/superhero were to make an appearance, they'd be public enemy number one.
Until Satan/Zod shows the world who the real enemy is, of course